Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 61 of 356
Found at i:19574096 original size:20 final size:20
Alignment explanation
Indices: 19574071--19574112 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
19574061 GAAAGAACAA
19574071 ACTAAAGAGAAAATATCAAT
1 ACTAAAGAGAAAATATCAAT
19574091 ACTAAAGAGAAAATATCAAT
1 ACTAAAGAGAAAATATCAAT
19574111 AC
1 AC
19574113 AATGAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.19
Consensus pattern (20 bp):
ACTAAAGAGAAAATATCAAT
Found at i:19575704 original size:69 final size:69
Alignment explanation
Indices: 19575549--19575742 Score: 209
Period size: 67 Copynumber: 2.9 Consensus size: 69
19575539 AAGTGATAAT
* * * * **
19575549 TTCTTCACTATTTTCCTTAAAAAAAGTTAATTTTAATCCCATATTGACTAAAGAATACTCTTATA
1 TTCTTCACTATTTTCATT-AAAAAATTTAATTTTAATCCCACACTGACTAAAGAATACTCGGATA
19575614 ACTCA
65 ACTCA
* * * *
19575619 --CTTCACTATTTTCATTAAAAAATTTATTTTTAATTCCACACTGATTAGAGAATACT-GGATAA
1 TTCTTCACTATTTTCATTAAAAAATTTAATTTTAATCCCACACTGACTAAAGAATACTCGGATAA
19575681 CTCA
66 CTCA
* * * *
19575685 CTTCTTCACTATTTTCATTAAAAAA--TAATTTTAATCCCTCATTGGCTAGAGAATACTC
1 -TTCTTCACTATTTTCATTAAAAAATTTAATTTTAATCCCACACTGACTAAAGAATACTC
19575743 CCAGGCTCCA
Statistics
Matches: 104, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
66 8 0.08
67 59 0.57
68 15 0.14
69 22 0.21
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.40
Consensus pattern (69 bp):
TTCTTCACTATTTTCATTAAAAAATTTAATTTTAATCCCACACTGACTAAAGAATACTCGGATAA
CTCA
Found at i:19575851 original size:12 final size:13
Alignment explanation
Indices: 19575824--19575849 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19575814 TCATTATTTC
19575824 ATTAAAAAGTTAA
1 ATTAAAAAGTTAA
19575837 ATTAAAAAGTTAA
1 ATTAAAAAGTTAA
19575850 TTTTAATCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
ATTAAAAAGTTAA
Found at i:19576050 original size:14 final size:14
Alignment explanation
Indices: 19576033--19576060 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19576023 AAAAAGTTAA
19576033 TTTTAATCCCACAT
1 TTTTAATCCCACAT
19576047 TTTTAATCCCACAT
1 TTTTAATCCCACAT
19576061 AATTAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTTAATCCCACAT
Found at i:19581186 original size:9 final size:9
Alignment explanation
Indices: 19581172--19581199 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19581162 ATTTATATTT
19581172 TATTAAAAA
1 TATTAAAAA
19581181 TATTAAAAA
1 TATTAAAAA
19581190 TATTAAAAA
1 TATTAAAAA
19581199 T
1 T
19581200 TTTACCGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TATTAAAAA
Found at i:19581589 original size:130 final size:131
Alignment explanation
Indices: 19581228--19581872 Score: 992
Period size: 131 Copynumber: 4.9 Consensus size: 131
19581218 ACATTTATTT
* * * * *
19581228 TAATAAAAATTATTGGCTAATTTAAAAGAACATTTATTGTATTAAAATTAAAAAAAGTAAAGTAC
1 TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAATTAAAGTAC
* *
19581293 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAAAATAAATATAAAA
66 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAAAA
19581358 A
131 A
* * * *
19581359 TAAAAAAAAATATTGACTAATTTAAAAGAATATTTATTTTAATAAAATTAAAAAAATTAAAGTAA
1 TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAATTAAAGTAC
19581424 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAAAA
66 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAAAA
19581489 A
131 A
* *
19581490 TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAAAAAAATT-AAAATATTAAAGTAC
1 TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAATTAAAGTAC
* * *
19581554 AATTAAAATATTAAAAACAACTTTTATTTTTTTAATTCAAACTATATAAAAATTTAAATATAAAA
66 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAAAA
19581619 A
131 A
*
19581620 TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAATTGAAA-TA
1 TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAATT-AAAGTA
19581684 CAATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATA-AAA
65 CAATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAAA
19581748 AA
130 AA
* * * *
19581750 TAATAAAAAATATTGCCTAATCTAAAAAAACATTTATCTTAATAAAATTTTTAAAAAAAAAGTAA
1 TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAATAAAA---TT--AAAAAAATTAA
* *
19581815 AGTACGATTAAAATATCAAAAACAACTTTTATTTTATT-ATATGAAACTATATAAAAAA
61 AGTACAATTAAAATATTAAAAACAACTTTTATTTTATTAAT-TGAAACTATATAAAAAA
19581873 AGTTTCTACA
Statistics
Matches: 473, Mismatches: 32, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
130 171 0.36
131 233 0.49
132 3 0.01
133 2 0.00
134 5 0.01
135 59 0.12
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (131 bp):
TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAATTAAAGTAC
AATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAAAA
A
Found at i:19581601 original size:261 final size:261
Alignment explanation
Indices: 19581228--19581873 Score: 1001
Period size: 261 Copynumber: 2.5 Consensus size: 261
19581218 ACATTTATTT
* * * **
19581228 TAATAAAAATTATTGGCTAATTTAAAAGAACATTTATTGTATTAAAATTAAAAAAAGTAAAGTAC
1 TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAAAAAAATTAAAAAAAGTAAAGTAC
19581293 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAAAATAAATATAAAA
66 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAAAATAAATATAAAA
*
19581358 ATAAAAAAAAATATTGACTAATTTAAAAGAATATTTATTTTAATAAAATTAAAAAAATT-AAAGT
131 ATAAAAAAAAATATTGACTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAATTGAAA-T
19581422 AAAATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAA
195 AAAATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATA-AA
19581487 AAA
259 AAA
* *
19581490 TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAAAAAAATT-AAAATATTAAAGTAC
1 TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAAAAAAATTAAAAAAAGTAAAGTAC
* * **
19581554 AATTAAAATATTAAAAACAACTTTTATTTTTTTAATTCAAACTATATAAAAATTTAAATATAAAA
66 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAAAATAAATATAAAA
* *
19581619 ATAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAATTGAAATA
131 ATAAAAAAAAATATTGACTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAATTGAAATA
*
19581684 CAATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATAAAAA
196 AAATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATAAAAA
19581749 A
261 A
* * * *
19581750 TAATAAAAAATATTGCCTAATCTAAAAAAACATTTATCTTAATAAAATTTTTAAAAAAAAAGTAA
1 TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAA-AAAA--ATT--AAAAAAAGTAA
* * *
19581815 AGTACGATTAAAATATCAAAAACAACTTTTATTTTATT-ATATGAAACTATATAAAAAAA
61 AGTACAATTAAAATATTAAAAACAACTTTTATTTTATTAAT-TAAAACTATATAAAAAAA
19581874 GTTTCTACAA
Statistics
Matches: 349, Mismatches: 27, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
260 44 0.13
261 196 0.56
262 47 0.13
263 2 0.01
265 2 0.01
266 58 0.17
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (261 bp):
TAATAAAAAATATTGCCTAATTTAAAAGAACATTTATTTTAAAAAAATTAAAAAAAGTAAAGTAC
AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAAAATAAATATAAAA
ATAAAAAAAAATATTGACTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAATTGAAATA
AAATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATAAAAA
A
Found at i:19582310 original size:18 final size:18
Alignment explanation
Indices: 19582283--19582320 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
19582273 GGAAAAGAAA
*
19582283 ACATAAAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
*
19582301 ACATATAAGGGCTAGGAT
1 ACATAAAAGGGCTAGGAT
19582319 AC
1 AC
19582321 GCAACTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:19582943 original size:7 final size:7
Alignment explanation
Indices: 19582927--19583009 Score: 123
Period size: 7 Copynumber: 12.0 Consensus size: 7
19582917 AAATATTAGT
*
19582927 TAAATCC
1 TAAATAC
19582934 TAAATAC
1 TAAATAC
*
19582941 TAAATCC
1 TAAATAC
19582948 TAAATAC
1 TAAATAC
*
19582955 TAAATCC
1 TAAATAC
19582962 TAAATAC
1 TAAATAC
*
19582969 TAAACAC
1 TAAATAC
19582976 TAAATAC
1 TAAATAC
19582983 T-AATAC
1 TAAATAC
19582989 TAAATAC
1 TAAATAC
19582996 TAAATAC
1 TAAATAC
19583003 TAAATAC
1 TAAATAC
19583010 GAAACGACTA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
6 6 0.09
7 62 0.91
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAATAC
Found at i:19584175 original size:22 final size:23
Alignment explanation
Indices: 19584132--19584185 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
19584122 ACTAATTCAA
19584132 AAAAATTTAAACAGAGCTTTTTTG-C
1 AAAAA-TTAAACAGAGC--TTTTGAC
*
19584157 AAAAATTAAAGAGAG-TTTTGAC
1 AAAAATTAAACAGAGCTTTTGAC
19584179 AAAAATT
1 AAAAATT
19584186 GAGAGAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.19
22 8 0.30
24 9 0.33
25 5 0.19
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.31
Consensus pattern (23 bp):
AAAAATTAAACAGAGCTTTTGAC
Found at i:19584214 original size:22 final size:22
Alignment explanation
Indices: 19584186--19584227 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
19584176 GACAAAAATT
19584186 GAGAGAAATT-TGAGAGAATTTG
1 GAGAG-AATTGTGAGAGAATTTG
19584208 GAGAGAATTGTGAGAGAATT
1 GAGAGAATTGTGAGAGAATT
19584228 GTGAAAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.26
Consensus pattern (22 bp):
GAGAGAATTGTGAGAGAATTTG
Found at i:19584231 original size:11 final size:10
Alignment explanation
Indices: 19584184--19584227 Score: 61
Period size: 11 Copynumber: 4.1 Consensus size: 10
19584174 TTGACAAAAA
19584184 TTGAGAGAAAT
1 TTGAGAG-AAT
19584195 TTGAGAGAAT
1 TTGAGAGAAT
19584205 TTGGAGAGAAT
1 TT-GAGAGAAT
19584216 TGTGAGAGAAT
1 T-TGAGAGAAT
19584227 T
1 T
19584228 GTGAAAGGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.16
11 25 0.81
12 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.30
Consensus pattern (10 bp):
TTGAGAGAAT
Found at i:19589754 original size:35 final size:35
Alignment explanation
Indices: 19589708--19589778 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
19589698 GTCAATCTAG
*
19589708 AGGTAAAGATAGATGCCGAGACAAATGGTGGAGAT
1 AGGTAAAGATAGATACCGAGACAAATGGTGGAGAT
19589743 AGGTAAAGATAGATACCGAGACAAATGGTGGAGAT
1 AGGTAAAGATAGATACCGAGACAAATGGTGGAGAT
19589778 A
1 A
19589779 CCGATCTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.08, G:0.32, T:0.17
Consensus pattern (35 bp):
AGGTAAAGATAGATACCGAGACAAATGGTGGAGAT
Found at i:19594458 original size:32 final size:32
Alignment explanation
Indices: 19594419--19594482 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
19594409 TTTTTACATG
19594419 GACAGATGCAACACCAAGCCTCAGATTGCTCA
1 GACAGATGCAACACCAAGCCTCAGATTGCTCA
19594451 GACAGATGCAACACCAAGCCTCAGATTGCTCA
1 GACAGATGCAACACCAAGCCTCAGATTGCTCA
19594483 CTGCGCATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (32 bp):
GACAGATGCAACACCAAGCCTCAGATTGCTCA
Found at i:19600509 original size:30 final size:30
Alignment explanation
Indices: 19600475--19600537 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
19600465 GATGAAATGC
19600475 AGCAGCATGCAAGTGACCAAGCAGTCCAGT
1 AGCAGCATGCAAGTGACCAAGCAGTCCAGT
19600505 AGCAGCATGCAAGTGACCAAGCAGTCCAGT
1 AGCAGCATGCAAGTGACCAAGCAGTCCAGT
19600535 AGC
1 AGC
19600538 TGTACGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.13
Consensus pattern (30 bp):
AGCAGCATGCAAGTGACCAAGCAGTCCAGT
Found at i:19606408 original size:21 final size:22
Alignment explanation
Indices: 19606384--19606433 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
19606374 CGCTGTTTCT
*
19606384 AATCTCACT-GCTACAGTATCC
1 AATCTCACTCGCTACAGTAACC
*
19606405 AATCTCA-TCGCTACAGTAACT
1 AATCTCACTCGCTACAGTAACC
19606426 AATCTCAC
1 AATCTCAC
19606434 CGCCACCGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (22 bp):
AATCTCACTCGCTACAGTAACC
Found at i:19608188 original size:35 final size:35
Alignment explanation
Indices: 19608143--19608214 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
19608133 GTTTTTAAGG
* * *
19608143 TTAGGGTTTTGCCAAAATAAGTTAGGGTTTAGTGT
1 TTAGGGTTTTGCCAAAACAAATTAGGGTTTAGAGT
* **
19608178 TTAGGTTTTTGTTAAAACAAATTAGGGTTTAGAGT
1 TTAGGGTTTTGCCAAAACAAATTAGGGTTTAGAGT
19608213 TT
1 TT
19608215 TAGTAGATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.43
Consensus pattern (35 bp):
TTAGGGTTTTGCCAAAACAAATTAGGGTTTAGAGT
Found at i:19608305 original size:34 final size:34
Alignment explanation
Indices: 19608250--19608336 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 34
19608240 ATTTTGTGTT
**
19608250 ATTTTATAA-AAATTATTTAAATTAAGG-TTTAGG
1 ATTTTA-AATAAATTAAGTAAATTAAGGTTTTAGG
*
19608283 ATTGTTAAATAAATTAAGTAAATTAGGGTTTTTAGG
1 ATT-TTAAATAAATTAAGTAAATTAAGG-TTTTAGG
*
19608319 GTTTTAAATAAATTAAGT
1 ATTTTAAATAAATTAAGT
19608337 TAGGGTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 5 0.11
34 18 0.39
35 15 0.33
36 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (34 bp):
ATTTTAAATAAATTAAGTAAATTAAGGTTTTAGG
Found at i:19608339 original size:22 final size:22
Alignment explanation
Indices: 19608314--19608357 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
19608304 ATTAGGGTTT
19608314 TTAGGGTTTTAAATAAATTAAG
1 TTAGGGTTTTAAATAAATTAAG
19608336 TTAGGGTTTTAAATAAATTAAG
1 TTAGGGTTTTAAATAAATTAAG
19608358 GTTTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (22 bp):
TTAGGGTTTTAAATAAATTAAG
Found at i:19608340 original size:31 final size:33
Alignment explanation
Indices: 19608277--19608345 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 33
19608267 TAAATTAAGG
19608277 TTTAGGATTGTTAAATAAATTAAGTAAATTAGGGTT
1 TTTAGGATTGTTAAATAAATTAAG---ATTAGGGTT
*
19608313 TTTAGGGTT-TTAAATAAATTAAG-TTAGGGTT
1 TTTAGGATTGTTAAATAAATTAAGATTAGGGTT
19608344 TT
1 TT
19608346 AAATAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 10 0.31
35 14 0.44
36 8 0.25
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (33 bp):
TTTAGGATTGTTAAATAAATTAAGATTAGGGTT
Found at i:19608362 original size:17 final size:17
Alignment explanation
Indices: 19608340--19608373 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19608330 ATTAAGTTAG
19608340 GGTTTTAAATAAATTAA
1 GGTTTTAAATAAATTAA
*
19608357 GGTTTTAAATAAGTTAA
1 GGTTTTAAATAAATTAA
19608374 ATTAGGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
GGTTTTAAATAAATTAA
Found at i:19608374 original size:22 final size:21
Alignment explanation
Indices: 19608314--19608383 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
19608304 ATTAGGGTTT
*
19608314 TTAGGGTTTTAAATAAATTAAG
1 TTAGGGTTTTAAAT-AATTAAA
19608336 TTAGGGTTTT--A-AA-TAAA
1 TTAGGGTTTTAAATAATTAAA
*
19608353 TTAAGGTTTTAAATAAGTTAAA
1 TTAGGGTTTTAAATAA-TTAAA
19608375 TTAGGGTTT
1 TTAGGGTTT
19608384 ATGGTTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 12 0.30
18 2 0.05
19 1 0.03
20 3 0.08
22 22 0.55
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
TTAGGGTTTTAAATAATTAAA
Found at i:19608401 original size:25 final size:25
Alignment explanation
Indices: 19608371--19608427 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
19608361 TTAAATAAGT
* * *
19608371 TAAATTAG-GGTTTATGGTTTTTAGA
1 TAAATTAGAGTTTTA-GGGTTTTAAA
19608396 TAAATTAGAGTTTTAGGGTTTTAAA
1 TAAATTAGAGTTTTAGGGTTTTAAA
19608421 TAAATTA
1 TAAATTA
19608428 AATTAGGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (25 bp):
TAAATTAGAGTTTTAGGGTTTTAAA
Found at i:19608851 original size:29 final size:30
Alignment explanation
Indices: 19608804--19608871 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
19608794 TGGCCTAAGA
* *
19608804 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
19608834 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
19608864 GCAAATAT
1 GTAAATAT
19608872 TTTAAGGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:19611308 original size:126 final size:127
Alignment explanation
Indices: 19610982--19611309 Score: 439
Period size: 127 Copynumber: 2.6 Consensus size: 127
19610972 GGGTATTGCA
* *
19610982 AGTAGTTCCTAAAAAAATAATTTTGAGAAA-ACGTTTCTGAACAAATAGTGTCAAAAACGCTTCA
1 AGTAGTTCATGAAAAAATAATTTTGA-AAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCA
* * * * **
19611046 AGCAGGATGTAGTATCAGCAAAATTACGGAAAAAAGCTATCACGTGGACTCTCTTTTTTCTAC
65 AGCAGGATGCACTACCAGCAAAATTACGGAAAAAAGCTACCACGCAGACTCTCTTTTTTCTAC
* *
19611109 AGTAGTTCATGAAAAAATAATTTTGAGAAGACGTTTTTGAACAAATAGTGTCAAAAACGCTTCAA
1 AGTAGTTCATGAAAAAATAATTTTGAAAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAA
* *
19611174 GCAGGATGCACTGCCAGCAAAATTACAGG-AAAAAGCTCCCACGCAGA-TGCTC-TTTTTCTAC
66 GCAGGATGCACTACCAGCAAAATTAC-GGAAAAAAGCTACCACGCAGACT-CTCTTTTTTCTAC
* * * * * *
19611235 AGTAGTTCTTGAAAAAATAATTTTGAAAAGATGTTTCTAAACAAATAATGTCAAAAATGTTTCAA
1 AGTAGTTCATGAAAAAATAATTTTGAAAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAA
19611300 GCAGGATGCA
66 GCAGGATGCA
19611310 ATATTGGAAA
Statistics
Matches: 178, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
126 79 0.44
127 97 0.54
128 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (127 bp):
AGTAGTTCATGAAAAAATAATTTTGAAAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAA
GCAGGATGCACTACCAGCAAAATTACGGAAAAAAGCTACCACGCAGACTCTCTTTTTTCTAC
Found at i:19611322 original size:126 final size:126
Alignment explanation
Indices: 19610982--19611372 Score: 457
Period size: 126 Copynumber: 3.1 Consensus size: 126
19610972 GGGTATTGCA
* *
19610982 AGTAGTTCCTAAAAAAATAATTTTGAGAAA-ACGTTTCTGAACAAATAGTGTCAAAAACGCTTCA
1 AGTAGTTCATGAAAAAATAATTTTGA-AAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCA
* * **
19611046 AGCAGGATGTAGTATCAGCAAAATTAC-GGAAAAAAGCTATCACGTGGACT-CTCTTTTTTCTAC
65 AGCAGGATGCAATATCAGCAAAATTACAGG-AAAAAGCTCCCACGTGGA-TGCTC-TTTTTCTAC
* *
19611109 AGTAGTTCATGAAAAAATAATTTTGAGAAGACGTTTTTGAACAAATAGTGTCAAAAACGCTTCAA
1 AGTAGTTCATGAAAAAATAATTTTGAAAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAA
* ** **
19611174 GCAGGATGCACTGCCAGCAAAATTACAGGAAAAAGCTCCCACGCAGATGCTCTTTTTCTAC
66 GCAGGATGCAATATCAGCAAAATTACAGGAAAAAGCTCCCACGTGGATGCTCTTTTTCTAC
* * * * * *
19611235 AGTAGTTCTTGAAAAAATAATTTTGAAAAGATGTTTCTAAACAAATAATGTCAAAAATGTTTCAA
1 AGTAGTTCATGAAAAAATAATTTTGAAAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAA
** * * * * * *
19611300 GCAGGATGCAATATTGGAAAAATTTCTA-AAAAAAACTCCCACGTGGACGCTCTTTTTCTAT
66 GCAGGATGCAATATCAGCAAAATTAC-AGGAAAAAGCTCCCACGTGGATGCTCTTTTTCTAC
*
19611361 AGTAGTTAATGA
1 AGTAGTTCATGA
19611373 TTGGCCTTAG
Statistics
Matches: 225, Mismatches: 35, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
126 125 0.56
127 98 0.44
128 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
AGTAGTTCATGAAAAAATAATTTTGAAAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAA
GCAGGATGCAATATCAGCAAAATTACAGGAAAAAGCTCCCACGTGGATGCTCTTTTTCTAC
Found at i:19615526 original size:7 final size:7
Alignment explanation
Indices: 19615516--19615540 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19615506 TTATATACAT
19615516 AATACTA
1 AATACTA
19615523 AATACTA
1 AATACTA
19615530 AATACTA
1 AATACTA
19615537 AATA
1 AATA
19615541 TGAAACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:19620035 original size:18 final size:20
Alignment explanation
Indices: 19620012--19620048 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
19620002 GAGCAATTAT
19620012 TTTTGTAAT-T-TTTTTTAG
1 TTTTGTAATATATTTTTTAG
19620030 TTTTGTAATATATTTTTTA
1 TTTTGTAATATATTTTTTA
19620049 TTTATTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (20 bp):
TTTTGTAATATATTTTTTAG
Found at i:19620079 original size:17 final size:17
Alignment explanation
Indices: 19620037--19620079 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
19620027 TAGTTTTGTA
*
19620037 ATATATTTTTTATTTAT
1 ATATATTTATTATTTAT
*
19620054 -TCATTTTTATTATTTAT
1 AT-ATATTTATTATTTAT
19620071 ATATATTTA
1 ATATATTTA
19620080 AAATTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATATTTATTATTTAT
Found at i:19623177 original size:13 final size:13
Alignment explanation
Indices: 19623143--19623170 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19623133 TTTAATTATA
19623143 ATAATATAATAAT
1 ATAATATAATAAT
19623156 ATAATATAATAAT
1 ATAATATAATAAT
19623169 AT
1 AT
19623171 TTTATAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:19626617 original size:14 final size:15
Alignment explanation
Indices: 19626598--19626630 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19626588 GGGGCAAAGC
*
19626598 TAAAAAT-CTTGAAT
1 TAAAAATGCTTAAAT
19626612 TAAAAATGCTTAAAT
1 TAAAAATGCTTAAAT
19626627 TAAA
1 TAAA
19626631 TTATTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (15 bp):
TAAAAATGCTTAAAT
Found at i:19630584 original size:18 final size:18
Alignment explanation
Indices: 19630561--19630595 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19630551 CTGCTTCTAA
*
19630561 AATCTGTTTTTTCTTTTC
1 AATCTGTGTTTTCTTTTC
19630579 AATCTGTGTTTTCTTTT
1 AATCTGTGTTTTCTTTT
19630596 GCTCTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (18 bp):
AATCTGTGTTTTCTTTTC
Found at i:19636337 original size:45 final size:45
Alignment explanation
Indices: 19636144--19636399 Score: 302
Period size: 46 Copynumber: 5.6 Consensus size: 45
19636134 ATTGAAGGAA
* *
19636144 GCCATAATGTCTTTCAACCATGGTCTTATTCTCTTTTCGATATGAT
1 GCCATAGTGTCTTTCAACCATGGTCTTATTC-ATTTTCGATATGAT
* *
19636190 GCCATAGTGCCTTTCAACCATGGTTTTATTCATTTTCTGATATGAT
1 GCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTC-GATATGAT
*
19636236 GCCATAG-GTTCTTTCAACCATGGTCTTATTCGTTTTCCGATATGAT
1 GCCATAGTG-TCTTTCAACCATGGTCTTATTCATTTT-CGATATGAT
* * *
19636282 CCCATAGTGTCTTTCAACCATAGTCTTATTCATTTTCGATAGGAT
1 GCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATATGAT
* * *
19636327 GCCATAGTGTCTTTCAACTATGGTCTTACTCA-TCT-GAATCATGAT
1 GCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCG-AT-ATGAT
* * * *
19636372 GACATAGCGTCTTTCAGCTATGGTCTTA
1 GCCATAGTGTCTTTCAACCATGGTCTTA
19636400 CTCGTTTGAA
Statistics
Matches: 184, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.01
44 4 0.02
45 71 0.39
46 106 0.58
47 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (45 bp):
GCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATATGAT
Found at i:19636400 original size:45 final size:45
Alignment explanation
Indices: 19636324--19636418 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
19636314 TTTTCGATAG
* * *
19636324 GATGCCATAGTGTCTTTCAACTATGGTCTTACTCATCTGAATCAT
1 GATGACATAGCGTCTTTCAACTATGGTCTTACTCATCTGAATAAT
* * *
19636369 GATGACATAGCGTCTTTCAGCTATGGTCTTACTCGTTTGAATAAT
1 GATGACATAGCGTCTTTCAACTATGGTCTTACTCATCTGAATAAT
19636414 GATGA
1 GATGA
19636419 ACCGACTCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (45 bp):
GATGACATAGCGTCTTTCAACTATGGTCTTACTCATCTGAATAAT
Found at i:19637235 original size:21 final size:20
Alignment explanation
Indices: 19637197--19637236 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19637187 ATTTAACAAC
*
19637197 AAAACTTAAAAATCTATCAT
1 AAAACTTAAAAATATATCAT
*
19637217 AAAACTTCATAAATATATCA
1 AAAACTT-AAAAATATATCA
19637237 AATTCATCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAACTTAAAAATATATCAT
Found at i:19642426 original size:42 final size:42
Alignment explanation
Indices: 19642379--19642474 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
19642369 TGATGATGAC
* *
19642379 TCGGTTATTTATGGGTACTTAGTGTGCGAAATTGAGATAGCT
1 TCGGTTATATATGGGCACTTAGTGTGCGAAATTGAGATAGCT
** * *
19642421 TCGGTTATATATTTGCATTTAGTGTGCGAGATTGAGATAGCT
1 TCGGTTATATATGGGCACTTAGTGTGCGAAATTGAGATAGCT
* *
19642463 TCGCTTGTATAT
1 TCGGTTATATAT
19642475 ACACATTGGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.41
Consensus pattern (42 bp):
TCGGTTATATATGGGCACTTAGTGTGCGAAATTGAGATAGCT
Found at i:19642494 original size:48 final size:42
Alignment explanation
Indices: 19642397--19642501 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 42
19642387 TTATGGGTAC
* * *
19642397 TTAGTGTGCGAAATTGAGATAGCTTCGGTTATATATTTGCAT
1 TTAGTGTGCGAAATTGAGATAGCTTCGGTTATACATTGGCAA
*
19642439 TTAGTGTGCGAGATTGAGATAGCTTCGCTTGTATATACACATTGGCAA
1 TTAGTGTGCGAAATTGAGATAGCTTCG---GT-TAT--ACATTGGCAA
19642487 TTAGTGTGCGAAATT
1 TTAGTGTGCGAAATT
19642502 AATACAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
42 26 0.50
45 2 0.04
46 3 0.06
48 21 0.40
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.37
Consensus pattern (42 bp):
TTAGTGTGCGAAATTGAGATAGCTTCGGTTATACATTGGCAA
Found at i:19643990 original size:26 final size:22
Alignment explanation
Indices: 19643942--19644008 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 22
19643932 GACGAAGTGA
19643942 TTGTATAATTGTTTTAT-AAGT
1 TTGTATAATTGTTTTATAAAGT
19643963 TTGTATAATTGTTTTATAAGTCCAGT
1 TTGTATAATTGTTTTATAA----AGT
19643989 TTGTATAATTGTTTTATAAA
1 TTGTATAATTGTTTTATAAA
19644009 TCTAGTAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
21 17 0.41
22 2 0.05
26 22 0.54
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.54
Consensus pattern (22 bp):
TTGTATAATTGTTTTATAAAGT
Found at i:19650790 original size:29 final size:30
Alignment explanation
Indices: 19650761--19650816 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
19650751 ATATATTTGA
*
19650761 AATCTAG-TCTTTT-ATTTTTAATTTTATG
1 AATCTAGCCCTTTTGATTTTTAATTTTATG
* *
19650789 AATTTAGCCCTTTTGATTTTTAAATTTA
1 AATCTAGCCCTTTTGATTTTTAATTTTA
19650817 AAAATATAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.26
29 5 0.22
30 12 0.52
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.57
Consensus pattern (30 bp):
AATCTAGCCCTTTTGATTTTTAATTTTATG
Found at i:19656981 original size:21 final size:21
Alignment explanation
Indices: 19656939--19656982 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
19656929 CAATCCTGAC
* * *
19656939 AATTCCAACAAAAAATCGTAA
1 AATTCAAAAAAAAAATAGTAA
*
19656960 AATTCAAAAAAAAAATATTAA
1 AATTCAAAAAAAAAATAGTAA
19656981 AA
1 AA
19656983 GGGTAGAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.66, C:0.11, G:0.02, T:0.20
Consensus pattern (21 bp):
AATTCAAAAAAAAAATAGTAA
Found at i:19665681 original size:26 final size:26
Alignment explanation
Indices: 19665620--19665687 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
19665610 TTAAATTAAT
* *
19665620 TAATTATTATTATT-TTATTATCTTC
1 TAATTATTATTATTAGTACTATCTTC
*
19665645 TAATTTTTTATTATTAGTACTAT-TTC
1 TAA-TTATTATTATTAGTACTATCTTC
19665671 ATAATTATTATATATTA
1 -TAATTATTAT-TATTA
19665688 CTATTACATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 3 0.09
26 19 0.54
27 13 0.37
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.60
Consensus pattern (26 bp):
TAATTATTATTATTAGTACTATCTTC
Found at i:19665801 original size:34 final size:34
Alignment explanation
Indices: 19665759--19665834 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
19665749 TTATACTATA
* *
19665759 ATTA-TATTTACTTT-TATGGTTACCATTATTTTT
1 ATTATTATTT-CTTTATATCGTTACCATTATTATT
* **
19665792 ATTATTATTTCTTTATATCTTTGTCATTATTATT
1 ATTATTATTTCTTTATATCGTTACCATTATTATT
19665826 ATTATTATT
1 ATTATTATT
19665835 ATTATTATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 8 0.22
34 28 0.78
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (34 bp):
ATTATTATTTCTTTATATCGTTACCATTATTATT
Found at i:19665825 original size:3 final size:3
Alignment explanation
Indices: 19665817--19665854 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19665807 TATCTTTGTC
19665817 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19665855 AATACTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19666424 original size:3 final size:3
Alignment explanation
Indices: 19666416--19666640 Score: 50
Period size: 3 Copynumber: 77.7 Consensus size: 3
19666406 AAATTAATTA
* * * * *
19666416 ATT ATT ATT ATT -TT ATT A-T CTT CTA ATT -TT -TT ATT ATT AGT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
19666460 ATT -TC ATA ATT ATT ATAT ATT ACT ATT A-C ATT CATT -TT TTT A-T
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT -ATT ATT ATT ATT
* * * ** *
19666503 ATT CTT TTT ATT AAT ATT ATT ACC ACT ATT ATT ATT ATT ATT -TT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
19666549 ACT ATA ATT A-T ATTT ACTT -TT ATG GTT ATC ATT ATT TTT ATT ATT
1 ATT ATT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
19666594 ATT -TCT -TT A-T ATCT -TT GTC ATT ATT AGCTT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT AT-T ATT ATT ATT ATT A--TT ATT ATT ATT ATT ATT
19666639 AT
1 AT
19666641 CATACTTTCT
Statistics
Matches: 162, Mismatches: 39, Indels: 42
0.67 0.16 0.17
Matches are distributed among these distances:
2 26 0.16
3 122 0.75
4 11 0.07
5 3 0.02
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:19666475 original size:26 final size:26
Alignment explanation
Indices: 19666414--19666481 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
19666404 TTAAATTAAT
* *
19666414 TAATTATTATTATT-TTATTATCTTC
1 TAATTATTATTATTAGTACTATCTTC
*
19666439 TAATTTTTTATTATTAGTACTAT-TTC
1 TAA-TTATTATTATTAGTACTATCTTC
19666465 ATAATTATTATATATTA
1 -TAATTATTAT-TATTA
19666482 CTATTACATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 3 0.09
26 19 0.54
27 13 0.37
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.60
Consensus pattern (26 bp):
TAATTATTATTATTAGTACTATCTTC
Found at i:19668794 original size:46 final size:46
Alignment explanation
Indices: 19668727--19668946 Score: 232
Period size: 46 Copynumber: 4.8 Consensus size: 46
19668717 TAACCCGCCT
* *
19668727 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCC
* *
19668773 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCCGCCTAGTT-ACAT-C
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTC-G--GAC-A-TTCGCATCC
* * * ** *
19668822 -TCA-TGAACTCGTACTCAACTCAACGAGTTCAAACGTTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCC
* * **
19668866 ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGTTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCC
*
19668912 ATAAGTGAACTCAGACTCAACTCAACGAGCTCGGA
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
19668947 TGCCCAAATA
Statistics
Matches: 147, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 2 0.01
45 2 0.01
46 101 0.69
47 26 0.18
48 2 0.01
49 3 0.02
50 4 0.03
51 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCC
Found at i:19672730 original size:41 final size:41
Alignment explanation
Indices: 19672671--19672775 Score: 149
Period size: 41 Copynumber: 2.6 Consensus size: 41
19672661 AGATTAATGA
* *
19672671 TGAATTGCACATATGTGCCCCTGTTTGTACTTCGGTA-CCT
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCT
*
19672711 CTGAATTGCACATACGTGCCCTTGTTTGTACTTCGATACCCT
1 -TGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCT
* *
19672753 TGAATTACACATACATGCCCCTG
1 TGAATTGCACATACGTGCCCCTG
19672776 ATTATACTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 54 0.95
42 3 0.05
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCT
Found at i:19672929 original size:203 final size:203
Alignment explanation
Indices: 19672580--19672987 Score: 755
Period size: 203 Copynumber: 2.0 Consensus size: 203
19672570 ATTATTGAGG
* *
19672580 TAAGTTCGTAGTTTCTTTAATACGTAACAAATTTTTATTTGCGCACTTGTACTATGATGTTTTAA
1 TAAGTTCGTAGTGTCTTTAATACGTAACAAATTTTTATTTGCGCACTTGTACTATGATGCTTTAA
*
19672645 TTATTAATTTTTTAGAAGATTAATGATGAATTGCACATATGTGCCCCTGTTTGTACTTCGGTACC
66 TTATTAATTTTTTAGAAGATTAATGATGAATTGCACATATGTGCCCCTGTTTGTACTTCAGTACC
19672710 TCTGAATTGCACATACGTGCCCTTGTTTGTACTTCGATACCCTTGAATTACACATACATGCCCCT
131 TCTGAATTGCACATACGTGCCCTTGTTTGTACTTCGATACCCTTGAATTACACATACATGCCCCT
19672775 GATTATAC
196 GATTATAC
*
19672783 TAAGTTCGTAGTGT-TTTAATAGGTAACAAATTTTTATTTGCGCACTTGTACTATGATGCTTTAA
1 TAAGTTCGTAGTGTCTTTAATACGTAACAAATTTTTATTTGCGCACTTGTACTATGATGCTTTAA
19672847 TTATTAATTTTTTTAGAAGATTAATGATGAATTGCACATATGTGCCCCTGTTTGTACTTCAGTAC
66 TTATTAA-TTTTTTAGAAGATTAATGATGAATTGCACATATGTGCCCCTGTTTGTACTTCAGTAC
*
19672912 CTCTGAATTGCACATACGTGCCCTTGTTTGTACTTCGATACCCTTGAATTGCACATACATGCCCC
130 CTCTGAATTGCACATACGTGCCCTTGTTTGTACTTCGATACCCTTGAATTACACATACATGCCCC
19672977 TGATTATAC
195 TGATTATAC
19672986 TA
1 TA
19672988 CGGTACCCCT
Statistics
Matches: 199, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
202 55 0.28
203 144 0.72
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (203 bp):
TAAGTTCGTAGTGTCTTTAATACGTAACAAATTTTTATTTGCGCACTTGTACTATGATGCTTTAA
TTATTAATTTTTTAGAAGATTAATGATGAATTGCACATATGTGCCCCTGTTTGTACTTCAGTACC
TCTGAATTGCACATACGTGCCCTTGTTTGTACTTCGATACCCTTGAATTACACATACATGCCCCT
GATTATAC
Found at i:19672995 original size:41 final size:42
Alignment explanation
Indices: 19672874--19672995 Score: 158
Period size: 41 Copynumber: 3.0 Consensus size: 42
19672864 AGATTAATGA
* *
19672874 TGAATTGCACATATGTGCCCCTGTTTGTACTTCAGTA-CCTC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTC
* *
19672915 TGAATTGCACATACGTGCCCTTGTTTGTACTTCGATACCCT-
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTC
* * * *
19672956 TGAATTGCACATACATGCCCCTGATTATACTACGGTACCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
19672996 CTGGATATAC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
41 67 0.96
42 3 0.04
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (42 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTC
Found at i:19678504 original size:64 final size:64
Alignment explanation
Indices: 19678354--19678484 Score: 235
Period size: 64 Copynumber: 2.0 Consensus size: 64
19678344 AGTCAGTCGT
* *
19678354 AGTCATAGTCTACGAAATTCTCATGGGTACAAGTACCTTCCAGTCAGATAGTACAATTACATTC
1 AGTCACAGTCTACGAAATTCTCATGGGTACAAGTACCTTCCAGTCAGATAGTACAATCACATTC
*
19678418 AGTCACAGTCTACGAAATTCTCATGGGTACAAGTGCCTTCCAGTCAGATAGTACAATCACATTC
1 AGTCACAGTCTACGAAATTCTCATGGGTACAAGTACCTTCCAGTCAGATAGTACAATCACATTC
19678482 AGT
1 AGT
19678485 GACAATGTTA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (64 bp):
AGTCACAGTCTACGAAATTCTCATGGGTACAAGTACCTTCCAGTCAGATAGTACAATCACATTC
Found at i:19682325 original size:18 final size:18
Alignment explanation
Indices: 19682282--19682326 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
19682272 GGCCTATTAC
*
19682282 AGTAACAATAAATAGTGT
1 AGTAACAGTAAATAGTGT
19682300 AGTAACAGT-AATCAGTGT
1 AGTAACAGTAAAT-AGTGT
19682318 AGTAACAGT
1 AGTAACAGT
19682327 TTAAACAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (18 bp):
AGTAACAGTAAATAGTGT
Found at i:19682700 original size:27 final size:27
Alignment explanation
Indices: 19682665--19682819 Score: 213
Period size: 27 Copynumber: 5.7 Consensus size: 27
19682655 GGAAAAACAA
* *
19682665 TCATCTTACCATATAAGAGCAAAATAG
1 TCATTTTACCATATAAGGGCAAAATAG
* *
19682692 TCATTTTACCACATAAGGGCAAAACAG
1 TCATTTTACCATATAAGGGCAAAATAG
19682719 TCATTTTACCATATAAGGGCAAAATAG
1 TCATTTTACCATATAAGGGCAAAATAG
* *
19682746 TCATTTTACCACATAAGGGCAAAAACAG
1 TCATTTTACCATATAAGGGC-AAAATAG
* *
19682774 CCATTTTACCATATAAGGACAAAATAG
1 TCATTTTACCATATAAGGGCAAAATAG
19682801 TCATTTTACCA-ATTAAGGG
1 TCATTTTACCATA-TAAGGG
19682820 TCTAGGTATG
Statistics
Matches: 112, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 88 0.79
28 23 0.21
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (27 bp):
TCATTTTACCATATAAGGGCAAAATAG
Found at i:19682729 original size:54 final size:54
Alignment explanation
Indices: 19682657--19682819 Score: 249
Period size: 54 Copynumber: 3.0 Consensus size: 54
19682647 ATCACATAGG
* *
19682657 AAAAACAATCATCTTACCATATAAGAGCAAAATAGTCATTTTACCACATAAGGGC
1 AAAAACAGTCATTTTACCATATAAG-GCAAAATAGTCATTTTACCACATAAGGGC
19682712 -AAAACAGTCATTTTACCATATAAGGGCAAAATAGTCATTTTACCACATAAGGGC
1 AAAAACAGTCATTTTACCATATAA-GGCAAAATAGTCATTTTACCACATAAGGGC
*
19682766 AAAAACAGCCATTTTACCATATAAGGACAAAATAGTCATTTTACCA-ATTAAGGG
1 AAAAACAGTCATTTTACCATATAAGG-CAAAATAGTCATTTTACCACA-TAAGGG
19682820 TCTAGGTATG
Statistics
Matches: 101, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
54 53 0.52
55 48 0.48
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (54 bp):
AAAAACAGTCATTTTACCATATAAGGCAAAATAGTCATTTTACCACATAAGGGC
Found at i:19682797 original size:55 final size:54
Alignment explanation
Indices: 19682670--19682819 Score: 241
Period size: 55 Copynumber: 2.8 Consensus size: 54
19682660 AACAATCATC
*
19682670 TTACCATATAA-GAGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATT
1 TTACCATATAAGGA-CAAAATAGTCATTTTACCACATAAGGGCAAAACAGCCATT
*
19682724 TTACCATATAAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAAACAGCCATT
1 TTACCATATAAGGACAAAATAGTCATTTTACCACATAAGGGC-AAAACAGCCATT
19682779 TTACCATATAAGGACAAAATAGTCATTTTACCA-ATTAAGGG
1 TTACCATATAAGGACAAAATAGTCATTTTACCACA-TAAGGG
19682820 TCTAGGTATG
Statistics
Matches: 90, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
54 40 0.44
55 50 0.56
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (54 bp):
TTACCATATAAGGACAAAATAGTCATTTTACCACATAAGGGCAAAACAGCCATT
Found at i:19695007 original size:49 final size:50
Alignment explanation
Indices: 19694816--19695012 Score: 193
Period size: 50 Copynumber: 3.9 Consensus size: 50
19694806 TTTTATTGTG
***
19694816 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATACGTACCCA-ATAACTT
1 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGATAA-TT
* * * * * * * **
19694867 CGATCACGTATGTAATACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
19694917 AGGTC-AAGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCGCA-TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
19694967 -GGTCGCATGTTTAGTACTAAGTGCAGGCTACTATGGGTACCAGATA
1 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
19695013 GCTTTGGCTA
Statistics
Matches: 116, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
49 39 0.34
50 44 0.38
51 33 0.28
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (50 bp):
AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:19698780 original size:20 final size:20
Alignment explanation
Indices: 19698757--19698804 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
19698747 TATCATTGGC
** *
19698757 TATAATATTATTTGAATAGT
1 TATAATATTAAATGAATAAT
19698777 TATAATATTAAATGAATAAT
1 TATAATATTAAATGAATAAT
19698797 TAT-ATATT
1 TATAATATT
19698805 TTTAAGACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (20 bp):
TATAATATTAAATGAATAAT
Found at i:19701828 original size:6 final size:7
Alignment explanation
Indices: 19701812--19701837 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19701802 GCAAATTTGC
19701812 AAAATTA
1 AAAATTA
19701819 AAAATTA
1 AAAATTA
19701826 AAAATTA
1 AAAATTA
19701833 AAAAT
1 AAAAT
19701838 ACTGTGAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:19705488 original size:19 final size:20
Alignment explanation
Indices: 19705449--19705486 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19705439 CTAGTGTTAC
19705449 ATTTTAAAATTTAAAAAAAT
1 ATTTTAAAATTTAAAAAAAT
*
19705469 ATTTTAAAATTCAAAAAA
1 ATTTTAAAATTTAAAAAA
19705487 TAAACTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTTTAAAATTTAAAAAAAT
Found at i:19707138 original size:16 final size:16
Alignment explanation
Indices: 19707091--19707138 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
19707081 TTTTAAAATT
*
19707091 ATAAATAATATAATGG
1 ATAAATAATATAATAG
*
19707107 AT-AAT-ATA-AA-AC
1 ATAAATAATATAATAG
19707119 ATAAATAATATAATAG
1 ATAAATAATATAATAG
19707135 ATAA
1 ATAA
19707139 TATATGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
12 2 0.08
13 5 0.20
14 6 0.24
15 5 0.20
16 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (16 bp):
ATAAATAATATAATAG
Found at i:19707150 original size:28 final size:28
Alignment explanation
Indices: 19707084--19707142 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
19707074 TTACAAATTT
*
19707084 TAAAATTATAAATAATATAATGGATAATA
1 TAAAA-TATAAATAATATAATAGATAATA
*
19707113 TAAAACATAAATAATATAATAGATAATA
1 TAAAATATAAATAATATAATAGATAATA
19707141 TA
1 TA
19707143 TGATATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (28 bp):
TAAAATATAAATAATATAATAGATAATA
Found at i:19707190 original size:11 final size:11
Alignment explanation
Indices: 19707174--19707210 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
19707164 AAAAGGTAAT
19707174 ATATAATAAAA
1 ATATAATAAAA
19707185 ATATAAT-AAA
1 ATATAATAAAA
*
19707195 ATATAATATAA
1 ATATAATAAAA
19707206 ATATA
1 ATATA
19707211 TGTGATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATATAATAAAA
Found at i:19707195 original size:28 final size:27
Alignment explanation
Indices: 19707156--19707208 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
19707146 TATAACATAT
*
19707156 AATATAAAAAAAGGTAATATATAATAAA
1 AATATAAAAAAAGATAATATA-AATAAA
* *
19707184 AATATAATAAAATATAATATAAATA
1 AATATAAAAAAAGATAATATAAATA
19707209 TATGTGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (27 bp):
AATATAAAAAAAGATAATATAAATAAA
Found at i:19709152 original size:205 final size:205
Alignment explanation
Indices: 19708800--19709175 Score: 599
Period size: 205 Copynumber: 1.8 Consensus size: 205
19708790 AATCTGCTTC
* *
19708800 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTTCTCCAGCATAAGCACG
1 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTCCAGCATAAACACG
* * * * * *
19708865 CGAAAACCAAATTAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTG
66 CGAAAACCAAATCAGCTACGTCTTCGACTCGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
* **
19708930 GATCTACTTCAGTATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCCCCGTTGAAGTGGA
131 GATCTACTTCAGTATAAACATCTAAAGGCCAGATCTGCTATGTATCTGCTCCCCGTTGAAGTGGA
19708995 GATGCCAGAA
196 GATGCCAGAA
* * *
19709005 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACG
1 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTCCAGCATAAACACG
* *
19709070 TGAAATCCAAATCAGCTACGTCTTCGACTCGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
66 CGAAAACCAAATCAGCTACGTCTTCGACTCGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
*
19709135 GATCTGCTTCAGTATAAACATCTAAAGGCCAGATCTGCTAT
131 GATCTACTTCAGTATAAACATCTAAAGGCCAGATCTGCTAT
19709176 ACTGCGGCCT
Statistics
Matches: 154, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
205 154 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (205 bp):
TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTCCAGCATAAACACG
CGAAAACCAAATCAGCTACGTCTTCGACTCGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
GATCTACTTCAGTATAAACATCTAAAGGCCAGATCTGCTATGTATCTGCTCCCCGTTGAAGTGGA
GATGCCAGAA
Found at i:19717195 original size:14 final size:16
Alignment explanation
Indices: 19717160--19717196 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
19717150 CAAACGATGC
19717160 GATG-AAATGCTATGA
1 GATGCAAATGCTATGA
19717175 GATGCAAATGC-ATGA
1 GATGCAAATGCTATGA
19717190 -ATGCAAA
1 GATGCAAA
19717197 AGGATATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GATGCAAATGCTATGA
Found at i:19717239 original size:14 final size:14
Alignment explanation
Indices: 19717216--19717245 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19717206 ATTCTGGTTC
19717216 AACTTCATTTAGAA
1 AACTTCATTTAGAA
*
19717230 AACTTTATTTAGAA
1 AACTTCATTTAGAA
19717244 AA
1 AA
19717246 ATAATATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
AACTTCATTTAGAA
Found at i:19720791 original size:29 final size:29
Alignment explanation
Indices: 19720736--19720792 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
19720726 TAAATAAATG
* *
19720736 ATATACAAAATATATAAAAGAATTAGTAT
1 ATATACAAAATATATAAAAAAAGTAGTAT
19720765 ATATA-AAAATATATAAAATAAAGTAGTA
1 ATATACAAAATATATAAAA-AAAGTAGTA
19720793 ATTGTTAACG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (29 bp):
ATATACAAAATATATAAAAAAAGTAGTAT
Found at i:19721156 original size:40 final size:41
Alignment explanation
Indices: 19721100--19721196 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 41
19721090 ACAAATTTAC
* * * *
19721100 AAATTATAAATAATATAATG-GATAATATAAAACATAAATA
1 AAATAATAGATAATATAATGAGATAACATAAAACATAAAAA
* * * *
19721140 ATATAATAGATAATAT-ATGATATAACATATAATATAAAAA
1 AAATAATAGATAATATAATGAGATAACATAAAACATAAAAA
*
19721180 AAATAATAGGTAATATA
1 AAATAATAGATAATATA
19721197 TAATAAAATA
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
39 3 0.07
40 42 0.93
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (41 bp):
AAATAATAGATAATATAATGAGATAACATAAAACATAAAAA
Found at i:19721197 original size:40 final size:40
Alignment explanation
Indices: 19721133--19721213 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
19721123 AATATAAAAC
* * * *
19721133 ATAAATAATATAATAGATAATATATGATATAACATATAAT
1 ATAAAAAAAATAATAGATAATATATAATAAAACATATAAT
* *
19721173 ATAAAAAAAATAATAGGTAATATATAATAAAATATATAAT
1 ATAAAAAAAATAATAGATAATATATAATAAAACATATAAT
19721213 A
1 A
19721214 AAATATAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (40 bp):
ATAAAAAAAATAATAGATAATATATAATAAAACATATAAT
Found at i:19721199 original size:14 final size:12
Alignment explanation
Indices: 19721191--19721232 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
19721181 AATAATAGGT
19721191 AATATATAATAA
1 AATATATAATAA
19721203 AATATATAAT-A
1 AATATATAATAA
19721214 AA-ATATAATATA
1 AATATATAATA-A
19721226 AATATAT
1 AATATAT
19721233 GTGATAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 13 0.48
13 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AATATATAATAA
Found at i:19721200 original size:7 final size:7
Alignment explanation
Indices: 19721121--19721232 Score: 56
Period size: 7 Copynumber: 16.3 Consensus size: 7
19721111 AATATAATGG
19721121 ATAATAT
1 ATAATAT
* *
19721128 AAAACAT
1 ATAATAT
19721135 A-AATAAT
1 ATAAT-AT
*
19721142 ATAATAG
1 ATAATAT
19721149 ATAATAT
1 ATAATAT
*
19721156 AT--GAT
1 ATAATAT
*
19721161 ATAACAT
1 ATAATAT
19721168 ATAATAT
1 ATAATAT
* * *
19721175 AAAAAAA
1 ATAATAT
*
19721182 ATAATAG
1 ATAATAT
*
19721189 GTAATAT
1 ATAATAT
19721196 ATAATA-
1 ATAATAT
19721202 A-AATAT
1 ATAATAT
19721208 ATAATAAAAT
1 ATAAT---AT
19721218 ATAATAT
1 ATAATAT
19721225 A-AATAT
1 ATAATAT
19721231 AT
1 AT
19721233 GTGATAAATT
Statistics
Matches: 78, Mismatches: 17, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
5 8 0.10
6 10 0.13
7 50 0.64
8 3 0.04
10 7 0.09
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (7 bp):
ATAATAT
Found at i:19723894 original size:19 final size:18
Alignment explanation
Indices: 19723842--19723894 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
19723832 CTCTCTCAAT
19723842 AAAAATTATAAAAAATTCA
1 AAAAATTAT-AAAAATTCA
** *
19723861 AAACAAACATTAAAATTCA
1 AAA-AATTATAAAAATTCA
19723880 AAAAATTTATAAAAA
1 AAAAA-TTATAAAAA
19723895 ATTTCAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 2 0.08
19 20 0.77
20 4 0.15
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATTATAAAAATTCA
Found at i:19724382 original size:21 final size:21
Alignment explanation
Indices: 19724358--19724397 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19724348 TTTTAAAGCG
19724358 TTTGTTCTTTTTCTTCTTCCA
1 TTTGTTCTTTTTCTTCTTCCA
19724379 TTTGTTCTTTTTCTTCTTC
1 TTTGTTCTTTTTCTTCTTC
19724398 TTCTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.03, C:0.23, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTGTTCTTTTTCTTCTTCCA
Found at i:19724398 original size:27 final size:26
Alignment explanation
Indices: 19724366--19724427 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
19724356 CGTTTGTTCT
*
19724366 TTTTCTTCTTCCATTTGTTCTTTTTC
1 TTTTCTTCTTCCATTTGCTCTTTTTC
**
19724392 TTCTTCTTCTTCTTTTTGCTCTTTTTC
1 TT-TTCTTCTTCCATTTGCTCTTTTTC
19724419 TTTT-TTCTT
1 TTTTCTTCTT
19724428 TCTAATAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.16
26 4 0.12
27 23 0.72
ACGTcount: A:0.02, C:0.23, G:0.03, T:0.73
Consensus pattern (26 bp):
TTTTCTTCTTCCATTTGCTCTTTTTC
Found at i:19724420 original size:18 final size:18
Alignment explanation
Indices: 19724362--19724408 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 18
19724352 AAAGCGTTTG
*
19724362 TTCTTTTTCTTCTTCCATTTG
1 TTCTTTTTCTTCTT-C--TTC
19724383 TTCTTTTTCTTCTTCTTC
1 TTCTTTTTCTTCTTCTTC
19724401 TTCTTTTT
1 TTCTTTTT
19724409 GCTCTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 10 0.40
20 1 0.04
21 14 0.56
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.72
Consensus pattern (18 bp):
TTCTTTTTCTTCTTCTTC
Found at i:19725906 original size:5 final size:5
Alignment explanation
Indices: 19725886--19725936 Score: 54
Period size: 5 Copynumber: 10.2 Consensus size: 5
19725876 GTATTTATAC
19725886 ATATT AT-TT CATATT ATATT ATATT ATATT AGT-TT ATATT AGT-TT
1 ATATT ATATT -ATATT ATATT ATATT ATATT A-TATT ATATT A-TATT
19725931 ATATT A
1 ATATT A
19725937 GTTTAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
4 4 0.10
5 32 0.80
6 4 0.10
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:19725937 original size:10 final size:10
Alignment explanation
Indices: 19725899--19725941 Score: 70
Period size: 10 Copynumber: 4.3 Consensus size: 10
19725889 TTATTTCATA
19725899 TTATATTA-T
1 TTATATTAGT
19725908 ATTATATTAGT
1 -TTATATTAGT
19725919 TTATATTAGT
1 TTATATTAGT
19725929 TTATATTAGT
1 TTATATTAGT
19725939 TTA
1 TTA
19725942 ATAATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 31 0.97
11 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (10 bp):
TTATATTAGT
Found at i:19726026 original size:17 final size:18
Alignment explanation
Indices: 19725999--19726035 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
19725989 GAAAAACAGA
*
19725999 AAAGAAAAAGAAGGAAAG
1 AAAGAAAAAGAAAGAAAG
19726017 AAAG-AAAAGAAAGAAAG
1 AAAGAAAAAGAAAGAAAG
19726034 AA
1 AA
19726036 GGAGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGAAAGAAAG
Found at i:19726041 original size:23 final size:22
Alignment explanation
Indices: 19725996--19726042 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
19725986 AACGAAAAAC
19725996 AGAAAAGAAAAAGAAGGAAAGAA
1 AGAAAAGAAAAAGAAGG-AAGAA
19726019 AGAAAAGAAAGAAAGAAGG-AGAA
1 AGAAAAG-AA-AAAGAAGGAAGAA
19726042 A
1 A
19726043 TTAGGGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.55
24 2 0.09
25 8 0.36
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AGAAAAGAAAAAGAAGGAAGAA
Found at i:19731996 original size:13 final size:13
Alignment explanation
Indices: 19731978--19732002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19731968 GATATTTCAG
19731978 TCATTCAGTTATT
1 TCATTCAGTTATT
19731991 TCATTCAGTTAT
1 TCATTCAGTTAT
19732003 GGGTTTAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TCATTCAGTTATT
Found at i:19732162 original size:70 final size:70
Alignment explanation
Indices: 19732049--19732192 Score: 270
Period size: 70 Copynumber: 2.1 Consensus size: 70
19732039 CAATCGTCTC
*
19732049 GGGCAACCTATGCAACCTTAGCTACAAATTAGTGGAAATGAGCTCACACGCCCATGTTGTATGCC
1 GGGCAACCTATGCAACCTTAGCTACAAATCAGTGGAAATGAGCTCACACGCCCATGTTGTATGCC
19732114 TGTGT
66 TGTGT
*
19732119 GGGCAACCTGTGCAACCTTAGCTACAAATCAGTGGAAATGAGCTCACACGCCCATGTTGTATGCC
1 GGGCAACCTATGCAACCTTAGCTACAAATCAGTGGAAATGAGCTCACACGCCCATGTTGTATGCC
19732184 TGTGT
66 TGTGT
19732189 GGGC
1 GGGC
19732193 CCATAGGTCC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (70 bp):
GGGCAACCTATGCAACCTTAGCTACAAATCAGTGGAAATGAGCTCACACGCCCATGTTGTATGCC
TGTGT
Found at i:19734870 original size:13 final size:13
Alignment explanation
Indices: 19734852--19734885 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
19734842 TGGTTTAATC
*
19734852 AATTGATTTTATT
1 AATTGATTTGATT
19734865 AATTGATTTGATT
1 AATTGATTTGATT
19734878 AATT-ATTT
1 AATTGATTT
19734886 ATTTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (13 bp):
AATTGATTTGATT
Found at i:19740642 original size:22 final size:22
Alignment explanation
Indices: 19740615--19740667 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
19740605 GTCATGCATT
*
19740615 TTTTTATTTGCTATTAT-TTAC
1 TTTTTATTTACTATTATCTTAC
* *
19740636 TTATTTATTTATTATTGTCTTAC
1 TT-TTTATTTACTATTATCTTAC
19740659 TTTTTATTT
1 TTTTTATTT
19740668 TAAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 19 0.70
23 6 0.22
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTTTATTTACTATTATCTTAC
Found at i:19744221 original size:16 final size:16
Alignment explanation
Indices: 19744200--19744233 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
19744190 TTTGGGTCAT
19744200 GTGGTATATGCTGAGG
1 GTGGTATATGCTGAGG
19744216 GTGGTATATGCTGAGG
1 GTGGTATATGCTGAGG
19744232 GT
1 GT
19744234 ATTCGTATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.44, T:0.32
Consensus pattern (16 bp):
GTGGTATATGCTGAGG
Found at i:19748548 original size:19 final size:20
Alignment explanation
Indices: 19748519--19748561 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
19748509 CTTTATTTGC
19748519 ATGATGTGCTTACCGATTGT
1 ATGATGTGCTTACCGATTGT
*
19748539 ATGA-GTGCTTACCGATTTT
1 ATGATGTGCTTACCGATTGT
19748558 ATGA
1 ATGA
19748562 CATATTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (20 bp):
ATGATGTGCTTACCGATTGT
Found at i:19750456 original size:19 final size:19
Alignment explanation
Indices: 19750432--19750469 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19750422 TTTGGGTGTT
19750432 GGCCAACTAATGGCCGGCA
1 GGCCAACTAATGGCCGGCA
*
19750451 GGCCAACTGATGGCCGGCA
1 GGCCAACTAATGGCCGGCA
19750470 CCCACTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.34, T:0.11
Consensus pattern (19 bp):
GGCCAACTAATGGCCGGCA
Found at i:19750622 original size:54 final size:55
Alignment explanation
Indices: 19750555--19750683 Score: 188
Period size: 54 Copynumber: 2.4 Consensus size: 55
19750545 TTTTTTTCGT
* ** * *
19750555 GTGCTGGGACACTGATGGTCGGCTTCCTTGTACCAGATTTGAGAAAAAAATTT-G
1 GTGCTGGGACACTGATGGCCGGCACCCTTGTACCAAATTTGAAAAAAAAATTTGG
*
19750609 GTGCTAGGACACTGATGGCCGGCACCCTTGTACCAAATTTGAAAAAAAAATTTGG
1 GTGCTGGGACACTGATGGCCGGCACCCTTGTACCAAATTTGAAAAAAAAATTTGG
*
19750664 GTGCTGGGACACTAATGGCC
1 GTGCTGGGACACTGATGGCC
19750684 CTTGTATATT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 47 0.71
55 19 0.29
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (55 bp):
GTGCTGGGACACTGATGGCCGGCACCCTTGTACCAAATTTGAAAAAAAAATTTGG
Found at i:19751225 original size:21 final size:21
Alignment explanation
Indices: 19751200--19751246 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
19751190 TTTGTTGGTC
*
19751200 AAATTTTATATTTTCGTATAT
1 AAATTTTATATTTTCGTAAAT
19751221 AAATTTTATATTTTCGTAAAT
1 AAATTTTATATTTTCGTAAAT
19751242 AAATT
1 AAATT
19751247 ATTCTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (21 bp):
AAATTTTATATTTTCGTAAAT
Found at i:19751335 original size:21 final size:21
Alignment explanation
Indices: 19751310--19751356 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
19751300 TTTGTTGGTC
* *
19751310 AAATTTTATATTTTCGTATAT
1 AAATTTTATATTTTCATAAAT
19751331 AAATTTTATATTTTCATAAAT
1 AAATTTTATATTTTCATAAAT
19751352 AAATT
1 AAATT
19751357 ATTCTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
AAATTTTATATTTTCATAAAT
Found at i:19751341 original size:110 final size:110
Alignment explanation
Indices: 19751113--19751468 Score: 617
Period size: 110 Copynumber: 3.2 Consensus size: 110
19751103 TTGTTAGCTG
19751113 AATTTTATATTTTCGTAAATAAATTATTCTAAAATGTTT-ATATTATTTTGGGGTGCTGT-AAAA
1 AATTTTATATTTTCGTAAATAAATTATTCTAAAATGTTTGA-ATTATTTTGGGGTGCTGTAAAAA
* *
19751176 TATTTTAATTCTTATTTGTTGGTCAAATTTTATATTTTCGTATATA
65 TATTTTAATCCGTATTTGTTGGTCAAATTTTATATTTTCGTATATA
*
19751222 AATTTTATATTTTCGTAAATAAATTATTCTAAAATATTTGAATTATTTTGGGGTGCTGTAAAAAT
1 AATTTTATATTTTCGTAAATAAATTATTCTAAAATGTTTGAATTATTTTGGGGTGCTGTAAAAAT
19751287 ATTTTAATCCGTATTTGTTGGTCAAATTTTATATTTTCGTATATA
66 ATTTTAATCCGTATTTGTTGGTCAAATTTTATATTTTCGTATATA
* * *
19751332 AATTTTATATTTTCATAAATAAATTATTCTAAAATGTTCGAATTATTTTGGGATGCTGTAAAAAT
1 AATTTTATATTTTCGTAAATAAATTATTCTAAAATGTTTGAATTATTTTGGGGTGCTGTAAAAAT
*
19751397 ATTTTAATCCGTATTTGTTGGTCGAATTTTATATTTTCGTATATA
66 ATTTTAATCCGTATTTGTTGGTCAAATTTTATATTTTCGTATATA
*
19751442 AATTTTATATTTTCGTATATAAATTAT
1 AATTTTATATTTTCGTAAATAAATTAT
19751469 ATATTTTTTC
Statistics
Matches: 235, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
109 56 0.24
110 179 0.76
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (110 bp):
AATTTTATATTTTCGTAAATAAATTATTCTAAAATGTTTGAATTATTTTGGGGTGCTGTAAAAAT
ATTTTAATCCGTATTTGTTGGTCAAATTTTATATTTTCGTATATA
Found at i:19751478 original size:23 final size:21
Alignment explanation
Indices: 19751421--19751475 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
19751411 TTGTTGGTCG
19751421 AATTTTATATTTTCGTATATA
1 AATTTTATATTTTCGTATATA
19751442 AATTTTATATTTTCGTATATA
1 AATTTTATATTTTCGTATATA
*
19751463 AATTATATATTTT
1 AATTTTATATTTT
19751476 TTCATAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (21 bp):
AATTTTATATTTTCGTATATA
Found at i:19754304 original size:19 final size:19
Alignment explanation
Indices: 19754276--19754327 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
19754266 AAAATTCAAT
*
19754276 TAATTTTTAATTTAAACTA
1 TAATTATTAATTTAAACTA
* *
19754295 TAATTATTAAGTTAAACTT
1 TAATTATTAATTTAAACTA
19754314 TAATTATTTAATTT
1 TAATTA-TTAATTT
19754328 TAAAATTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (19 bp):
TAATTATTAATTTAAACTA
Found at i:19754415 original size:90 final size:90
Alignment explanation
Indices: 19754254--19754417 Score: 222
Period size: 90 Copynumber: 1.8 Consensus size: 90
19754244 TATTTCTATT
*
19754254 AATTAAAAATAAAAAATTCAATTAATTTTTAATTTAAACTATAATTATTAAGTTAAACTTTAATT
1 AATTAAAAATAAAAAATTCAATTAATTTTTAATTTAAACTATAATTATCAAGTTAAACTTTAATT
*
19754319 ATTTAATTTTAAAATTGATTTTTTA
66 AATTAATTTTAAAATTGATTTTTTA
* * * * * * * *
19754344 AATTAAAATTAAGAATTTCATTTCATTTTTAGTTTATACTTTAATTATCAAGTTAAACTTT-ATG
1 AATTAAAAATAAAAAATTCAATTAATTTTTAATTTAAACTATAATTATCAAGTTAAACTTTAAT-
19754408 TAATTAATTT
65 TAATTAATTT
19754418 ATTTACTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
89 2 0.03
90 61 0.97
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.49
Consensus pattern (90 bp):
AATTAAAAATAAAAAATTCAATTAATTTTTAATTTAAACTATAATTATCAAGTTAAACTTTAATT
AATTAATTTTAAAATTGATTTTTTA
Found at i:19754475 original size:13 final size:14
Alignment explanation
Indices: 19754457--19754485 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19754447 AATAATTGAA
19754457 TAATTTATTTA-TT
1 TAATTTATTTACTT
19754470 TAATTTATTTACTT
1 TAATTTATTTACTT
19754484 TA
1 TA
19754486 CACTATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
TAATTTATTTACTT
Found at i:19754512 original size:47 final size:47
Alignment explanation
Indices: 19754444--19754702 Score: 336
Period size: 47 Copynumber: 5.6 Consensus size: 47
19754434 TGTATTAAAT
19754444 TATAATAATTGAATAATTTATTTATTTAATTTATTTACTTTACACTA
1 TATAATAATTGAATAATTTATTTATTTAATTTATTTACTTTACACTA
* *** * *
19754491 TATAATAACTT-AACAATTTATTTATTTAAAACATTTATTTTGCACTA
1 TATAATAA-TTGAATAATTTATTTATTTAATTTATTTACTTTACACTA
19754538 TATAATAATTGAATAATTTATTTATTT-A-TT-TTTACTTTACACTA
1 TATAATAATTGAATAATTTATTTATTTAATTTATTTACTTTACACTA
* *** *
19754582 TATAATAATTTAATAATTTATTTATTTAAAACATTTATTTTACACTA
1 TATAATAATTGAATAATTTATTTATTTAATTTATTTACTTTACACTA
*
19754629 TATAATAACTT-AATAA-TT-TTT-TTTAATTTGTTTACTTTACACTA
1 TATAATAA-TTGAATAATTTATTTATTTAATTTATTTACTTTACACTA
19754673 TATAATAATTGAATAATTTATTTATTTAAT
1 TATAATAATTGAATAATTTATTTATTTAAT
19754703 AATTGGATAT
Statistics
Matches: 182, Mismatches: 20, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
43 2 0.01
44 69 0.38
45 6 0.03
46 8 0.04
47 93 0.51
48 4 0.02
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (47 bp):
TATAATAATTGAATAATTTATTTATTTAATTTATTTACTTTACACTA
Found at i:19754601 original size:91 final size:93
Alignment explanation
Indices: 19754444--19754701 Score: 409
Period size: 91 Copynumber: 2.8 Consensus size: 93
19754434 TGTATTAAAT
* *
19754444 TATAATAATTGAATAATTTATTTATTTAATTTATTTACTTTACACTATATAATAACTTAACAATT
1 TATAATAATTGAATAATTTATTTATTT-ATTTATTTACTTTACACTATATAATAATTTAATAATT
*
19754509 TATTTATTTAAAACATTTATTTTGCACTA
65 TATTTATTTAAAACATTTATTTTACACTA
19754538 TATAATAATTGAATAATTTATTTATTTA-TT-TTTACTTTACACTATATAATAATTTAATAATTT
1 TATAATAATTGAATAATTTATTTATTTATTTATTTACTTTACACTATATAATAATTTAATAATTT
19754601 ATTTATTTAAAACATTTATTTTACACTA
66 ATTTATTTAAAACATTTATTTTACACTA
* * *
19754629 TATAATAACTT-AATAATTT-TTT-TTAATTTGTTTACTTTACACTATATAATAATTGAATAATT
1 TATAATAA-TTGAATAATTTATTTATTTATTTATTTACTTTACACTATATAATAATTTAATAATT
19754691 TATTTATTTAA
65 TATTTATTTAA
19754702 TAATTGGATA
Statistics
Matches: 156, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
89 3 0.02
90 5 0.03
91 116 0.74
92 4 0.03
93 1 0.01
94 27 0.17
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (93 bp):
TATAATAATTGAATAATTTATTTATTTATTTATTTACTTTACACTATATAATAATTTAATAATTT
ATTTATTTAAAACATTTATTTTACACTA
Found at i:19758732 original size:29 final size:29
Alignment explanation
Indices: 19758699--19758756 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
19758689 GGCACTGTAA
*
19758699 GAACGTTTACATTGTAAGAAAGACAACTT
1 GAACGTTTACATTGCAAGAAAGACAACTT
*
19758728 GAACGTTTACATTGCAAGAAAGATAACTT
1 GAACGTTTACATTGCAAGAAAGACAACTT
19758757 ACTTCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (29 bp):
GAACGTTTACATTGCAAGAAAGACAACTT
Found at i:19760620 original size:19 final size:19
Alignment explanation
Indices: 19760596--19760646 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
19760586 AATCTTTAAG
19760596 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
19760615 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
19760634 GATATGCAATCTT
1 GATATGCAATCTT
19760647 GAAGATAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:19762204 original size:17 final size:18
Alignment explanation
Indices: 19762167--19762204 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
19762157 TCCTTTTTGC
*
19762167 ATTACATGTGTTTGTTTT
1 ATTACATGTGTTTGTTAT
19762185 ATTACATGTG-TTGTTAT
1 ATTACATGTGTTTGTTAT
19762202 ATT
1 ATT
19762205 CTAATACGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.58
Consensus pattern (18 bp):
ATTACATGTGTTTGTTAT
Found at i:19766314 original size:7 final size:7
Alignment explanation
Indices: 19766297--19766351 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
19766287 CTATTTCAAA
19766297 AAAAAAGG
1 AAAAAA-G
19766305 AAAAAAG
1 AAAAAAG
19766312 --AAAAG
1 AAAAAAG
*
19766317 CAAAAGAG
1 -AAAAAAG
19766325 AAAAAA-
1 AAAAAAG
19766331 ATAAAAAG
1 A-AAAAAG
19766339 AAAAAAG
1 AAAAAAG
19766346 AAAAAA
1 AAAAAA
19766352 ATGGAGAGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
5 5 0.12
6 1 0.03
7 23 0.57
8 11 0.28
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:19766321 original size:21 final size:21
Alignment explanation
Indices: 19766297--19766353 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
19766287 CTATTTCAAA
* *
19766297 AAAAAAGGAAAAAA-GAAAAG
1 AAAAAAGAAAAAAATAAAAAG
*
19766317 CAAAAGAGAAAAAAATAAAAAG
1 -AAAAAAGAAAAAAATAAAAAG
19766339 AAAAAAGAAAAAAAT
1 AAAAAAGAAAAAAAT
19766354 GGAGAGGCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.04
Consensus pattern (21 bp):
AAAAAAGAAAAAAATAAAAAG
Found at i:19767441 original size:84 final size:84
Alignment explanation
Indices: 19767300--19767699 Score: 639
Period size: 84 Copynumber: 4.8 Consensus size: 84
19767290 CAAAATTCAG
* * *
19767300 CGCCTTAATCCCCTAAGTAGTAGGGTAACAGGTTAAATTTACAGATCTTATCTCCCTAAGTAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
19767365 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
19767384 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
19767449 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
*
19767468 CGCCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
19767533 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
*
19767552 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGG-----TTCGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* * *
19767612 GCGAAACAGATCGACGACGACT
66 GTGGAGCAGATCGA--A-GACT
* * *
19767634 CACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGACCTTATCTCCCTAAGTAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
19767699 G
66 G
19767700 GGTAACAGGT
Statistics
Matches: 295, Mismatches: 13, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
79 38 0.13
81 1 0.00
82 35 0.12
84 195 0.66
87 26 0.09
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (84 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGAAGACT
Found at i:19767664 original size:44 final size:41
Alignment explanation
Indices: 19767353--19767664 Score: 162
Period size: 41 Copynumber: 7.5 Consensus size: 41
19767343 GATCTTATCT
* *
19767353 CCCTAAGTAGTAGTGG-AGCAGATCGA-AGACTCGCCTTAATC
1 CCCTAAGCAGTAG-GGTAACAGATCGACAGACTC-CCTTAATC
*
19767394 CCCTAAGCAGTAGGGTAACAGGTTAAATTTG-CAGA-T--CTT-ATC
1 CCCTAAGCAGTAGGGTAACA-G----A-TCGACAGACTCCCTTAATC
*
19767436 TCCCTAAGCAGTAGTGG-AGCAGATCGA-AGACTCGCCTTAATC
1 -CCCTAAGCAGTAG-GGTAACAGATCGACAGACTC-CCTTAATC
* *
19767478 CCCTAAGCGGTAGGGTAACAGGTTAAATTTG-CAGA-T--CTT-ATC
1 CCCTAAGCAGTAGGGTAACA-G----A-TCGACAGACTCCCTTAATC
*
19767520 TCCCTAAGCAGTAGTGG-AGCAGATCGA-AGACTCGCCTTAATC
1 -CCCTAAGCAGTAG-GGTAACAGATCGACAGACTC-CCTTAATC
*
19767562 CCCTAAGCAGTAGGGTAACAGGTTCG-CAGA-T--CTT-ATC
1 CCCTAAGCAGTAGGGTAACA-GATCGACAGACTCCCTTAATC
* *
19767599 TCCCTAAGCAGTAGCGAAACAGATCGACGACGACTCACCTTAATC
1 -CCCTAAGCAGTAGGGTAACAGATCGAC-A-GACTC-CCTTAATC
19767644 CCCTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGTAACAG
19767665 GTTAAATTTG
Statistics
Matches: 209, Mismatches: 18, Indels: 85
0.67 0.06 0.27
Matches are distributed among these distances:
37 17 0.08
38 26 0.12
39 1 0.00
40 8 0.04
41 54 0.26
42 23 0.11
43 37 0.18
44 26 0.12
45 3 0.01
46 4 0.02
47 10 0.05
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (41 bp):
CCCTAAGCAGTAGGGTAACAGATCGACAGACTCCCTTAATC
Found at i:19768287 original size:19 final size:19
Alignment explanation
Indices: 19768263--19768336 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
19768253 ATAATCTTCA
* *
19768263 ATGATATGCAATCATATAT
1 ATGATATGCAATCTTAGAT
19768282 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
19768301 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
19768319 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
19768337 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
18 18 0.35
19 34 0.65
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:19768310 original size:37 final size:38
Alignment explanation
Indices: 19768263--19768343 Score: 123
Period size: 37 Copynumber: 2.2 Consensus size: 38
19768253 ATAATCTTCA
*
19768263 ATGATATGCAATCATATATATGATATGCAATCTTAGAT
1 ATGATATGCAATCATAGATATGATATGCAATCTTAGAT
*
19768301 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCATAGATATGATATGCAATCTTAGAT
19768337 A-GATATG
1 ATGATATG
19768344 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 3 0.08
36 3 0.08
37 29 0.73
38 5 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (38 bp):
ATGATATGCAATCATAGATATGATATGCAATCTTAGAT
Found at i:19768362 original size:22 final size:22
Alignment explanation
Indices: 19768280--19768359 Score: 84
Period size: 18 Copynumber: 3.9 Consensus size: 22
19768270 GCAATCATAT
19768280 ATATGATATGCAATCTT---AG
1 ATATGATATGCAATCTTAGAAG
19768299 ATATGAT-TGCAATCTT---AG
1 ATATGATATGCAATCTTAGAAG
19768317 ATATGATATGCAATCTTAGAAG
1 ATATGATATGCAATCTTAGAAG
* *
19768339 ATATGATTTTGTAATCTTAGA
1 ATATGA-TATGCAATCTTAGA
19768360 GATTTAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
18 18 0.33
19 16 0.30
22 8 0.15
23 12 0.22
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
ATATGATATGCAATCTTAGAAG
Found at i:19768650 original size:17 final size:17
Alignment explanation
Indices: 19768625--19768660 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
19768615 ATGTTTCCCG
19768625 AATTTTTTTATATATTTT
1 AATTTTTTTATA-ATTTT
19768643 AATTTTTTTATAATTTT
1 AATTTTTTTATAATTTT
19768660 A
1 A
19768661 GTATCATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTTTTTTATAATTTT
Found at i:19771958 original size:8 final size:8
Alignment explanation
Indices: 19771945--19771987 Score: 68
Period size: 8 Copynumber: 5.1 Consensus size: 8
19771935 AGTCCCTATT
19771945 TCACAAAA
1 TCACAAAA
19771953 TCACAAAA
1 TCACAAAA
19771961 TTCACAAAA
1 -TCACAAAA
19771970 TCACAAAA
1 TCACAAAA
19771978 TTCACAAAA
1 -TCACAAAA
19771987 T
1 T
19771988 TTGCATATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 17 0.52
9 16 0.48
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (8 bp):
TCACAAAA
Found at i:19771966 original size:17 final size:17
Alignment explanation
Indices: 19771944--19771987 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
19771934 TAGTCCCTAT
19771944 TTCACAAAATCACAAAA
1 TTCACAAAATCACAAAA
19771961 TTCACAAAATCACAAAA
1 TTCACAAAATCACAAAA
19771978 TTCACAAAAT
1 TTCACAAAAT
19771988 TTGCATATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (17 bp):
TTCACAAAATCACAAAA
Found at i:19771967 original size:9 final size:9
Alignment explanation
Indices: 19771944--19771988 Score: 76
Period size: 9 Copynumber: 5.2 Consensus size: 9
19771934 TAGTCCCTAT
19771944 TTCACAAAA
1 TTCACAAAA
19771953 -TCACAAAA
1 TTCACAAAA
19771961 TTCACAAAA
1 TTCACAAAA
19771970 -TCACAAAA
1 TTCACAAAA
19771978 TTCACAAAA
1 TTCACAAAA
19771987 TT
1 TT
19771989 TGCATATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 16 0.47
9 18 0.53
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (9 bp):
TTCACAAAA
Found at i:19775174 original size:13 final size:14
Alignment explanation
Indices: 19775156--19775185 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
19775146 TTATGTTATA
19775156 TTTCTTTC-TTTTC
1 TTTCTTTCTTTTTC
19775169 TTTCTTTCTTTTTC
1 TTTCTTTCTTTTTC
19775183 TTT
1 TTT
19775186 TTCTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTCTTTCTTTTTC
Found at i:19776099 original size:12 final size:12
Alignment explanation
Indices: 19776082--19776106 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19776072 AGATATGTAT
19776082 AATTTAGTAATA
1 AATTTAGTAATA
19776094 AATTTAGTAATA
1 AATTTAGTAATA
19776106 A
1 A
19776107 CAGGATTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AATTTAGTAATA
Found at i:19777683 original size:17 final size:17
Alignment explanation
Indices: 19777657--19777696 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
19777647 CTTGAAAAGG
*
19777657 AAAACAAATGAATCTTA
1 AAAACGAATGAATCTTA
*
19777674 AAAACGAATGAATTTTA
1 AAAACGAATGAATCTTA
19777691 AAAACG
1 AAAACG
19777697 TAATAAAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (17 bp):
AAAACGAATGAATCTTA
Found at i:19778338 original size:29 final size:29
Alignment explanation
Indices: 19778296--19778354 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
19778286 ATCAAAATAT
19778296 GTTAGTGCTCAGGTTGCCTCCCGAGAAGC
1 GTTAGTGCTCAGGTTGCCTCCCGAGAAGC
19778325 GTTAGTGCTCAGGTTGCCTCCCGAGAAGC
1 GTTAGTGCTCAGGTTGCCTCCCGAGAAGC
19778354 G
1 G
19778355 CTTATTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.27, G:0.32, T:0.24
Consensus pattern (29 bp):
GTTAGTGCTCAGGTTGCCTCCCGAGAAGC
Found at i:19784877 original size:23 final size:23
Alignment explanation
Indices: 19784847--19784893 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
19784837 TCAGTTTGCA
19784847 CAAGTTCTAAAGATTGGATGGCC
1 CAAGTTCTAAAGATTGGATGGCC
*
19784870 CAAGTTCTAAAGATTGGTTGGCC
1 CAAGTTCTAAAGATTGGATGGCC
19784893 C
1 C
19784894 TTGTACCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (23 bp):
CAAGTTCTAAAGATTGGATGGCC
Found at i:19793702 original size:54 final size:54
Alignment explanation
Indices: 19793503--19793709 Score: 231
Period size: 54 Copynumber: 3.9 Consensus size: 54
19793493 TTTCCTTTCT
* * * ** *
19793503 GAACTTACCATTGCCATGTCTTGACATGGTCTTATGTGGTATCCTTGCCTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * *
19793556 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATG-GA-CCTTTCCCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATA
* * * *
19793609 GTAACTCATCAATGCCATGTCTTGACATGTTCTTACATGATTTCCTTGCCTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * *
19793664 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTT
19793710 ATCTTACCAA
Statistics
Matches: 129, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
51 2 0.02
52 9 0.07
53 33 0.26
54 73 0.57
55 10 0.08
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.36
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
Found at i:19798132 original size:26 final size:26
Alignment explanation
Indices: 19798086--19798135 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
19798076 TTAGCATTGC
*
19798086 TTTTGAGAAGTTCTATGGAAAAGTGA
1 TTTTGAGAAGTACTATGGAAAAGTGA
* *
19798112 TTTTGAGAAGTACTTTTGAAAAGT
1 TTTTGAGAAGTACTATGGAAAAGT
19798136 TTGGTTTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (26 bp):
TTTTGAGAAGTACTATGGAAAAGTGA
Found at i:19805839 original size:29 final size:30
Alignment explanation
Indices: 19805806--19805890 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 30
19805796 TTGTTGTATT
19805806 TTTTAAGATTTTAAAATTTAA-TCATTATAC
1 TTTTAAGATTTTAAAATTTAATTCATT-TAC
* * *
19805836 -TTTAA-TTTTTATTAATTGAATTCATTTAC
1 TTTTAAGATTTTA-AAATTTAATTCATTTAC
*
19805865 TTTTCAGATTTTAAAATTTAAGTTCA
1 TTTTAAGATTTTAAAATTTAA-TTCA
19805891 ACTACTAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
28 5 0.12
29 14 0.33
30 15 0.35
31 9 0.21
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTTAAGATTTTAAAATTTAATTCATTTAC
Found at i:19811850 original size:15 final size:15
Alignment explanation
Indices: 19811839--19811872 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
19811829 TATTATTTTC
19811839 ATGTTAATTATTAAT
1 ATGTTAATTATTAAT
*
19811854 ATGTTAATTATTATT
1 ATGTTAATTATTAAT
19811869 ATGT
1 ATGT
19811873 AGTGGGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (15 bp):
ATGTTAATTATTAAT
Found at i:19812891 original size:19 final size:20
Alignment explanation
Indices: 19812867--19812907 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
19812857 GAATTTAGGT
*
19812867 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
19812886 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
19812906 AA
1 AA
19812908 TTATGTAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:19818201 original size:24 final size:25
Alignment explanation
Indices: 19818145--19818203 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
19818135 ATTTTATGTT
19818145 TATATATTGT-ATATAGAAATAATTA
1 TATATATT-TAATATAGAAATAATTA
*
19818170 TATTTATTTAATATA-AAATAAATTA
1 TATATATTTAATATAGAAAT-AATTA
19818195 -ATATATTTA
1 TATATATTTA
19818204 TTTCAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (25 bp):
TATATATTTAATATAGAAATAATTA
Done.